Extracting long tracks and lineages from videomicroscopy requires an extremely low error rate, which is challenging on complex datasets of dense or deforming cells. Leveraging temporal context is key to overcoming this challenge. We propose DistNet2D, a new deep neural network (DNN) architecture for 2D cell segmentation and tracking that leverages both mid- and long-term temporal information. DistNet2D considers seven frames at the input and uses a post-processing procedure that exploits information from the entire video to correct segmentation errors. DistNet2D outperforms two recent methods on two experimental datasets, one containing densely packed bacterial cells and the other containing eukaryotic cells. It is integrated into an ImageJ-based graphical user interface for 2D data visualization, curation, and training. Finally, we demonstrate the performance of DistNet2D on correlating the size and shape of cells with their transport properties over large statistics, for both bacterial and eukaryotic cells.
The emergence of natural language processing has revolutionized the way users interact with tabular data, enabling a shift from traditional query languages and manual plotting to more intuitive, language-based interfaces. The rise of large language models (LLMs) such as ChatGPT and its successors has further advanced this field, opening new avenues for natural language processing techniques. This survey presents a comprehensive overview of natural language interfaces for tabular data querying and visualization, which allow users to interact with data using natural language queries. We introduce the fundamental concepts and techniques underlying these interfaces with a particular emphasis on semantic parsing, the key technology facilitating the translation from natural language to SQL queries or data visualization commands. We then delve into the recent advancements in Text-to-SQL and Text-to-Vis problems from the perspectives of datasets, methodologies, metrics, and system designs. This includes a deep dive into the influence of LLMs, highlighting their strengths, limitations, and potential for future improvements. Through this survey, we aim to provide a roadmap for researchers and practitioners interested in developing and applying natural language interfaces for data interaction in the era of large language models.
Data visualization is a powerful tool for exploring and communicating insights in various domains. To automate visualization choice for datasets, a task known as visualization recommendation has been proposed. Various machine-learning-based approaches have been developed for this purpose, but they often require a large corpus of dataset-visualization pairs for training and lack natural explanations for their results. To address this research gap, we propose LLM4Vis, a novel ChatGPT-based prompting approach to perform visualization recommendation and return human-like explanations using very few demonstration examples. Our approach involves feature description, demonstration example selection, explanation generation, demonstration example construction, and inference steps. To obtain demonstration examples with high-quality explanations, we propose a new explanation generation bootstrapping to iteratively refine generated explanations by considering the previous generation and template-based hint. Evaluations on the VizML dataset show that LLM4Vis outperforms or performs similarly to supervised learning models like Random Forest, Decision Tree, and MLP in both few-shot and zero-shot settings. The qualitative evaluation also shows the effectiveness of explanations generated by LLM4Vis. We make our code publicly available at \href{https://github.com/demoleiwang/LLM4Vis}{https://github.com/demoleiwang/LLM4Vis}.
This work leverages the U.S. Federal Aviation Administration's Traffic Flow Management System dataset and DV8, a recently developed tool for highly interactive visualization of air traffic data, to develop clustering algorithms for categorizing air traffic by their varying flight paths. Two clustering methodologies, a spatial-based geographic distance model, and a vector-based cosine similarity model, are demonstrated and compared for their clustering effectiveness. Examples of their applications reveal successful, realistic clustering based on automated clustering result determination and human-in-the-loop processes, with geographic distance algorithms performing better for enroute portions of flight paths and cosine similarity algorithms performing better for near-terminal operations, such as arrival paths. A point extraction technique is applied to improve computation efficiency.
Translation of natural language into syntactically correct commands for data visualization is an important application of natural language models and could be leveraged to many different tasks. A closely related effort is the task of translating natural languages into SQL queries, which in turn could be translated into visualization with additional information from the natural language query supplied\cite{Zhong:2017qr}. Contributing to the progress in this area of research, we built natural language translation models to construct simplified versions of data and visualization queries in a language called Vega Zero. In this paper, we explore the design and performance of these sequence to sequence transformer based machine learning model architectures using large language models such as BERT as encoders to predict visualization commands from natural language queries, as well as apply available T5 sequence to sequence models to the problem for comparison.
Matrix Factorization (MF) has found numerous applications in Machine Learning and Data Mining, including collaborative filtering recommendation systems, dimensionality reduction, data visualization, and community detection. Motivated by the recent successes of tropical algebra and geometry in machine learning, we investigate two problems involving matrix factorization over the tropical algebra. For the first problem, Tropical Matrix Factorization (TMF), which has been studied already in the literature, we propose an improved algorithm that avoids many of the local optima. The second formulation considers the approximate decomposition of a given matrix into the product of three matrices where a usual matrix product is followed by a tropical product. This formulation has a very interesting interpretation in terms of the learning of the utility functions of multiple users. We also present numerical results illustrating the effectiveness of the proposed algorithms, as well as an application to recommendation systems with promising results.
Stochastic neighbor embedding (SNE) methods $t$-SNE, UMAP are two most popular dimensionality reduction methods for data visualization. Contrastive learning, especially self-supervised contrastive learning (SSCL), has showed great success in embedding features from unlabeled data. The conceptual connection between SNE and SSCL has been exploited. In this work, within the scope of preserving neighboring information of a dataset, we extend the self-supervised contrastive approach to the fully-supervised setting, allowing us to effectively leverage label information. Clusters of samples belonging to the same class are pulled together in low-dimensional embedding space, while simultaneously pushing apart clusters of samples from different classes.
Data visualization has emerged as an effective tool for getting insights from massive datasets. Due to the hardness of manipulating the programming languages of data visualization, automatic data visualization generation from natural languages (Text-to-Vis) is becoming increasingly popular. Despite the plethora of research effort on the English Text-to-Vis, studies have yet to be conducted on data visualization generation from questions in Chinese. Motivated by this, we propose a Chinese Text-to-Vis dataset in the paper and demonstrate our first attempt to tackle this problem. Our model integrates multilingual BERT as the encoder, boosts the cross-lingual ability, and infuses the $n$-gram information into our word representation learning. Our experimental results show that our dataset is challenging and deserves further research.
PhysioZoo is a collaborative platform designed for the analysis of continuous physiological time series. The platform currently comprises four modules, each consisting of a library, a user interface, and a set of tutorials: (1) PhysioZoo HRV, dedicated to studying heart rate variability (HRV) in humans and other mammals; (2) PhysioZoo SPO2, which focuses on the analysis of digital oximetry biomarkers (OBM) using continuous oximetry (SpO2) measurements from humans; (3) PhysioZoo ECG, dedicated to the analysis of electrocardiogram (ECG) time series; (4) PhysioZoo PPG, designed to study photoplethysmography (PPG) time series. In this proceeding, we introduce the PhysioZoo platform as an open resource for digital physiological biomarkers engineering, facilitating streamlined analysis and data visualization of physiological time series while ensuring the reproducibility of published experiments. We welcome researchers to contribute new libraries for the analysis of various physiological time series, such as electroencephalography, blood pressure, and phonocardiography. You can access the resource at physiozoo.com. We encourage researchers to explore and utilize this platform to advance their studies in the field of continuous physiological time-series analysis.
Organizations of all kinds, whether public or private, profit-driven or non-profit, and across various industries and sectors, rely on dashboards for effective data visualization. However, the reliability and efficacy of these dashboards rely on the quality of the visual and data they present. Studies show that less than a quarter of dashboards provide information about their sources, which is just one of the expected metadata when provenance is seriously considered. Provenance is a record that describes people, organizations, entities, and activities that had a role in the production, influence, or delivery of a piece of data or an object. This paper aims to provide a provenance representation model, that entitles standardization, modeling, generation, capture, and visualization, specifically designed for dashboards and its visual and data components. The proposed model will offer a comprehensive set of essential provenance metadata that enables users to evaluate the quality, consistency, and reliability of the information presented on dashboards. This will allow a clear and precise understanding of the context in which a specific dashboard was developed, ultimately leading to better decision-making.
Scene representation networks (SRNs) have been recently proposed for compression and visualization of scientific data. However, state-of-the-art SRNs do not adapt the allocation of available network parameters to the complex features found in scientific data, leading to a loss in reconstruction quality. We address this shortcoming with an adaptively placed multi-grid SRN (APMGSRN) and propose a domain decomposition training and inference technique for accelerated parallel training on multi-GPU systems. We also release an open-source neural volume rendering application that allows plug-and-play rendering with any PyTorch-based SRN. Our proposed APMGSRN architecture uses multiple spatially adaptive feature grids that learn where to be placed within the domain to dynamically allocate more neural network resources where error is high in the volume, improving state-of-the-art reconstruction accuracy of SRNs for scientific data without requiring expensive octree refining, pruning, and traversal like previous adaptive models. In our domain decomposition approach for representing large-scale data, we train an set of APMGSRNs in parallel on separate bricks of the volume to reduce training time while avoiding overhead necessary for an out-of-core solution for volumes too large to fit in GPU memory. After training, the lightweight SRNs are used for realtime neural volume rendering in our open-source renderer, where arbitrary view angles and transfer functions can be explored. A copy of this paper, all code, all models used in our experiments, and all supplemental materials and videos are available at https://github.com/skywolf829/APMGSRN.
The Cameras for Allsky Meteor Surveillance (CAMS) project, funded by NASA starting in 2010, aims to map our meteor showers by triangulating meteor trajectories detected in low-light video cameras from multiple locations across 16 countries in both the northern and southern hemispheres. Its mission is to validate, discover, and predict the upcoming returns of meteor showers. Our research aimed to streamline the data processing by implementing an automated cloud-based AI-enabled pipeline and improve the data visualization to improve the rate of discoveries by involving the public in monitoring the meteor detections. This article describes the process of automating the data ingestion, processing, and insight generation using an interpretable Active Learning and AI pipeline. This work also describes the development of an interactive web portal (the NASA Meteor Shower portal) to facilitate the visualization of meteor radiant maps. To date, CAMS has discovered over 200 new meteor showers and has validated dozens of previously reported showers.
Data visualization (DV) has become the prevailing tool in the market due to its effectiveness into illustrating insights in vast amounts of data. To lower the barrier of using DVs, automatic DV tasks, such as natural language question (NLQ) to visualization translation (formally called text-to-vis), have been investigated in the research community. However, text-to-vis assumes the NLQ to be well-organized and expressed in a single sentence. However, in real-world settings, complex DV is needed through consecutive exchanges between the DV system and the users. In this paper, we propose a new task named CoVis, short for Conversational text-to-Visualization, aiming at constructing DVs through a series of interactions between users and the system. Since it is the task which has not been studied in the literature, we first build a benchmark dataset named Dial-NVBench, including dialogue sessions with a sequence of queries from a user and responses from the system. Then, we propose a multi-modal neural network named MMCoVisNet to answer these DV-related queries. In particular, MMCoVisNet first fully understands the dialogue context and determines the corresponding responses. Then, it uses adaptive decoders to provide the appropriate replies: (i) a straightforward text decoder is used to produce general responses, (ii) an SQL-form decoder is applied to synthesize data querying responses, and (iii) a DV-form decoder tries to construct the appropriate DVs. We comparatively evaluate MMCoVisNet with other baselines over our proposed benchmark dataset. Experimental results validate that MMCoVisNet performs better than existing baselines and achieves a state-of-the-art performance.
Tables are prevalent in real-world databases, requiring significant time and effort for humans to analyze and manipulate. The advancements in large language models (LLMs) have made it possible to interact with tables using natural language input, bringing this capability closer to reality. In this paper, we present TableGPT, a unified fine-tuned framework that enables LLMs to understand and operate on tables using external functional commands. It introduces the capability to seamlessly interact with tables, enabling a wide range of functionalities such as question answering, data manipulation (e.g., insert, delete, query, and modify operations), data visualization, analysis report generation, and automated prediction. TableGPT aims to provide convenience and accessibility to users by empowering them to effortlessly leverage tabular data. At the core of TableGPT lies the novel concept of global tabular representations, which empowers LLMs to gain a comprehensive understanding of the entire table beyond meta-information. By jointly training LLMs on both table and text modalities, TableGPT achieves a deep understanding of tabular data and the ability to perform complex operations on tables through chain-of-command instructions. Importantly, TableGPT offers the advantage of being a self-contained system rather than relying on external API interfaces. Moreover, it supports efficient data process flow, query rejection (when appropriate) and private deployment, enabling faster domain data fine-tuning and ensuring data privacy, which enhances the framework's adaptability to specific use cases.
Purpose: Machine learning models can only be reliably evaluated if training, validation, and test data splits are representative and not affected by the absence of classes of interest. Surgical workflow and instrument recognition tasks are complicated in this manner, because of heavy data imbalances resulting from different lengths of phases and their erratic occurrences. Furthermore, the issue becomes difficult as sub-properties that help define phases, like instrument (co-)occurrence, are usually not considered when defining the split. We argue that such sub-properties must be equally considered. Methods: This work presents a publicly available data visualization tool that enables interactive exploration of dataset splits for surgical phase and instrument recognition. It focuses on the visualization of the occurrence of phases, phase transitions, instruments, and instrument combinations across sets. Particularly, it facilitates the assessment and identification of sub-optimal dataset splits. Results: We performed an analysis of common Cholec80 dataset splits using the proposed application and were able to uncover phase transitions and combinations of instruments that were not represented in one of the sets. Additionally, we outlined possible improvements to the splits. A user study with ten participants demonstrated the ability of participants to solve a selection of data exploration tasks using the proposed application. Conclusion: In highly unbalanced class distributions, special care should be taken with respect to the selection of an appropriate dataset split. Our interactive data visualization tool presents a promising approach for the assessment of dataset splits for surgical phase and instrument recognition. Evaluation results show that it can enhance the development of machine learning models. The application is available at https://cardio-ai.github.io/endovis-ml/ .
The diffusion maps embedding of data lying on a manifold has shown success in tasks such as dimensionality reduction, clustering, and data visualization. In this work, we consider embedding data sets that were sampled from a manifold which is closed under the action of a continuous matrix group. An example of such a data set is images whose planar rotations are arbitrary. The G-invariant graph Laplacian, introduced in Part I of this work, admits eigenfunctions in the form of tensor products between the elements of the irreducible unitary representations of the group and eigenvectors of certain matrices. We employ these eigenfunctions to derive diffusion maps that intrinsically account for the group action on the data. In particular, we construct both equivariant and invariant embeddings, which can be used to cluster and align the data points. We demonstrate the utility of our construction in the problem of random computerized tomography.
Exploratory data analysis (EDA) is a vital procedure for data science projects. In this work, we introduce a stable equilibrium point (SEP) - based framework for improving the efficiency and solution quality of EDA. By exploiting the SEPs to be the representative points, our approach aims to generate high-quality clustering and data visualization for large-scale data sets. A very unique property of the proposed method is that the SEPs will directly encode the clustering properties of data sets. Compared with prior state-of-the-art clustering and data visualization methods, the proposed methods allow substantially improving computing efficiency and solution quality for large-scale data analysis tasks.
We introduce NightPulse, an interactive tool for Night-time light (NTL) data visualization and analytics, which enables researchers and stakeholders to explore and analyze NTL data with a user-friendly platform. Powered by efficient system architecture, NightPulse supports image segmentation, clustering, and change pattern detection to identify urban development and sprawl patterns. It captures temporal trends of NTL and semantics of cities, answering questions about demographic factors, city boundaries, and unusual differences.
The rise of big data has amplified the need for efficient, user-friendly automated machine learning (AutoML) tools. However, the intricacy of understanding domain-specific data and defining prediction tasks necessitates human intervention making the process time-consuming while preventing full automation. Instead, envision an intelligent agent capable of assisting users in conducting AutoML tasks through intuitive, natural conversations without requiring in-depth knowledge of the underlying machine learning (ML) processes. This agent's key challenge is to accurately comprehend the user's prediction goals and, consequently, formulate precise ML tasks, adjust data sets and model parameters accordingly, and articulate results effectively. In this paper, we take a pioneering step towards this ambitious goal by introducing a ChatGPT-based conversational data-science framework to act as a "personal data scientist". Precisely, we utilize Large Language Models (ChatGPT) to build a natural interface between the users and the ML models (Scikit-Learn), which in turn, allows us to approach this ambitious problem with a realistic solution. Our model pivots around four dialogue states: Data Visualization, Task Formulation, Prediction Engineering, and Result Summary and Recommendation. Each state marks a unique conversation phase, impacting the overall user-system interaction. Multiple LLM instances, serving as "micro-agents", ensure a cohesive conversation flow, granting us granular control over the conversation's progression. In summary, we developed an end-to-end system that not only proves the viability of the novel concept of conversational data science but also underscores the potency of LLMs in solving complex tasks. Interestingly, its development spotlighted several critical weaknesses in the current LLMs (ChatGPT) and highlighted substantial opportunities for improvement.
We introduce the Collection Space Navigator (CSN), a browser-based visualization tool to explore, research, and curate large collections of visual digital artifacts that are associated with multidimensional data, such as vector embeddings or tables of metadata. Media objects such as images are often encoded as numerical vectors, for e.g. based on metadata or using machine learning to embed image information. Yet, while such procedures are widespread for a range of applications, it remains a challenge to explore, analyze, and understand the resulting multidimensional spaces in a more comprehensive manner. Dimensionality reduction techniques such as t-SNE or UMAP often serve to project high-dimensional data into low dimensional visualizations, yet require interpretation themselves as the remaining dimensions are typically abstract. Here, the Collection Space Navigator provides a customizable interface that combines two-dimensional projections with a set of configurable multidimensional filters. As a result, the user is able to view and investigate collections, by zooming and scaling, by transforming between projections, by filtering dimensions via range sliders, and advanced text filters. Insights that are gained during the interaction can be fed back into the original data via ad hoc exports of filtered metadata and projections. This paper comes with a functional showcase demo using a large digitized collection of classical Western art. The Collection Space Navigator is open source. Users can reconfigure the interface to fit their own data and research needs, including projections and filter controls. The CSN is ready to serve a broad community.